/* -----------------------------------------------------------------------
   See COPYRIGHT.TXT and LICENSE.TXT for copyright and license information
   ----------------------------------------------------------------------- */
#include "plm_config.h"
#include <time.h>
#include "itkImageRegionIterator.h"

#include "itk_image_load.h"
#include "itk_mask.h"
#include "pcmd_mask.h"
#include "plm_clp.h"
#include "plm_image.h"

static void
mask_main (Mask_parms* parms)
{
    Plm_image *img;
    img = plm_image_load_native ((const char*) parms->input_fn);
    if (!img) {
	print_and_exit ("Error: could not open '%s' for read\n",
	    (const char*) parms->input_fn);
    }

    UCharImageType::Pointer mask = itk_image_load_uchar (parms->mask_fn, 0);

    switch (img->m_type) {
    case PLM_IMG_TYPE_ITK_UCHAR:
	img->m_itk_uchar = mask_image (img->m_itk_uchar, mask, 
	    parms->mask_operation, parms->mask_value);
	break;
    case PLM_IMG_TYPE_ITK_SHORT:
	img->m_itk_short = mask_image (img->m_itk_short, mask, 
	    parms->mask_operation, parms->mask_value);
	break;
    case PLM_IMG_TYPE_ITK_USHORT:
	img->m_itk_ushort = mask_image (img->m_itk_ushort, mask, 
	    parms->mask_operation, parms->mask_value);
	break;
    case PLM_IMG_TYPE_ITK_ULONG:
	img->m_itk_uint32 = mask_image (img->m_itk_uint32, mask, 
	    parms->mask_operation, parms->mask_value);
	break;
    case PLM_IMG_TYPE_ITK_FLOAT:
	img->m_itk_float = mask_image (img->m_itk_float, mask, 
	    parms->mask_operation, parms->mask_value);
	break;
    default:
	print_and_exit ("Unhandled conversion in mask_main\n");
	break;
    }

    if (parms->output_dicom) {
	img->save_short_dicom ((const char*) parms->output_fn, 0, 0);
    } else {
	if (parms->output_type) {
	    img->convert (parms->output_type);
	}
	img->save_image ((const char*) parms->output_fn);
    }

    delete img;
}

static void
usage_fn (dlib::Plm_clp* parser, int argc, char *argv[])
{
    printf ("Usage: plastimatch %s [options]\n", argv[1]);
    parser->print_options (std::cout);
    std::cout << std::endl;
}

static void
parse_fn (
    Mask_parms* parms, 
    dlib::Plm_clp* parser, 
    int argc, 
    char* argv[]
)
{
    /* Add --help, --version */
    parser->add_default_options ();

    /* Input files */
    parser->add_long_option ("", "input", 
	"input directory or filename; "
	"can be an image or dicom directory", 1, "");
    parser->add_long_option ("", "mask", 
	"input filename for mask image", 1, "");
    parser->add_long_option ("", "output", 
	"output filename (for image file) or "
	"directory (for dicom)", 1, "");

    /* Output options */
    parser->add_long_option ("", "output-format", 
	"arg should be \"dicom\" for dicom output", 1, "");
    parser->add_long_option ("", "output-type", 
	"type of output image, one of {uchar, short, float, ...}", 1, "");

    /* Algorithm options */
    parser->add_long_option ("", "mask-value", 
	"value to set for pixels with mask (for \"fill\"), "
	"or outside of mask (for \"mask\"", 1, "");

    /* Parse options */
    parser->parse (argc,argv);

    /* Handle --help, --version */
    parser->check_default_options ();

    /* Check for required options */
    parser->check_required ("input");
    parser->check_required ("mask");
    parser->check_required ("output");

    /* Input files */
    parms->input_fn = parser->get_string("input").c_str();
    parms->output_fn = parser->get_string("output").c_str();
    parms->mask_fn = parser->get_string("mask").c_str();

    /* Output options */
    if (parser->option("output-format")) {
	std::string arg = parser->get_string ("output-format");
	if (arg != "dicom") {
	    throw (dlib::error ("Error. Unknown --output-format argument: " 
		    + arg));
	}
    }
    if (parser->option("output-type")) {
	std::string arg = parser->get_string ("output-type");
	parms->output_type = plm_image_type_parse (arg.c_str());
	if (parms->output_type == PLM_IMG_TYPE_UNDEFINED) {
	    throw (dlib::error ("Error. Unknown --output-type argument: " 
		    + arg));
	}
    }

    /* Algorithm options */
    if (parser->option("mask-value")) {
	parms->mask_value = parser->get_float("mask-value");
    }
}

void
do_command_mask (int argc, char *argv[])
{
    Mask_parms parms;

    /* Check if we're doing fill or mask */
    if (!strcmp (argv[1], "mask")) {
	parms.mask_operation = MASK_OPERATION_MASK;
    } else {
	parms.mask_operation = MASK_OPERATION_FILL;
    }

    /* Parse command line parameters */
    plm_clp_parse (&parms, &parse_fn, &usage_fn, argc, argv, 1);

    /* Do the masking */
    mask_main (&parms);

    printf ("Finished!\n");
}
